15-72783505-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001365225.1(ADPGK):c.187G>A(p.Ala63Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000116 in 1,465,286 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A63S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001365225.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADPGK | NM_001365225.1 | c.187G>A | p.Ala63Thr | missense_variant | Exon 1 of 7 | ENST00000456471.3 | NP_001352154.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000546 AC: 4AN: 73266Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 41928
GnomAD4 exome AF: 0.00000762 AC: 10AN: 1312944Hom.: 0 Cov.: 31 AF XY: 0.00000310 AC XY: 2AN XY: 644988
GnomAD4 genome AF: 0.0000459 AC: 7AN: 152342Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.187G>A (p.A63T) alteration is located in exon 1 (coding exon 1) of the ADPGK gene. This alteration results from a G to A substitution at nucleotide position 187, causing the alanine (A) at amino acid position 63 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at